BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081210.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 10,412,412 number of mapped reads = 8,977,983 (86.22%) number of supplementary alignments = 88,205 (0.85%) number of secondary alignments = 0 number of mapped bases = 586,215,226 bp number of sequenced bases = 586,027,680 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,065,156 duplication rate = 7.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.8669 >>>>>>> ACTG content number of A's = 166,151,126 bp (28.35%) number of C's = 116,898,150 bp (19.95%) number of T's = 176,146,396 bp (30.06%) number of G's = 126,683,325 bp (21.62%) number of N's = 148,683 bp (0.03%) GC percentage = 41.56% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 6,476,957 number of insertions = 40,464 mapped reads with insertion percentage = 0.45% number of deletions = 118,162 mapped reads with deletion percentage = 1.3% homopolymer indels = 45.16% >>>>>>> Coverage mean coverageData = 0.1894X std coverageData = 2.6521X There is a 10.41% of reference with a coverageData >= 1X There is a 4.3% of reference with a coverageData >= 2X There is a 1.91% of reference with a coverageData >= 3X There is a 0.87% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.21% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 78866249 0.31641345038012963 5.976441165809911 chr2 243199373 7965924 0.03275470615625312 0.8918498877152505 chr3 198022430 46793257 0.23630281175723378 0.957567064471982 chr4 191154276 40191772 0.21025829419583583 0.7985967655319584 chr5 180915260 60262094 0.33309569353077234 0.921146940368846 chr6 171115067 32530103 0.19010659651613263 1.0525129298071367 chr7 159138663 58029268 0.36464594402178685 6.253124342352873 chr8 146364022 28672084 0.19589570994434685 3.2517299525308276 chr9 141213431 25524719 0.1807527713139411 1.3623946538969842 chr10 135534747 25923160 0.19126578662518182 3.3548368326047484 chr11 135006516 10091442 0.07474781439438079 1.0757908323474843 chr12 133851895 2188934 0.016353403140090022 0.4818765186329812 chr13 115169878 24530313 0.2129924371370785 0.7172821366218103 chr14 107349540 11513823 0.10725544795068521 1.034535259250605 chr15 102531392 10541237 0.10280984968974186 0.4873874626639978 chr16 90354753 17273839 0.191177978207743 0.9736633592507333 chr17 81195210 17124257 0.2109023056902002 1.095753299251432 chr18 78077248 4570070 0.05853267266797108 2.7470491067646248 chr19 59128983 8528984 0.14424371208955175 4.0235756025758596 chr20 63025520 7219154 0.11454334688551558 0.660080455114534 chr21 48129895 9764023 0.2028681550209075 0.8489100966115745 chr22 51304566 7395063 0.1441404455112241 0.5960358735497414 chrMT 16571 207215 12.504676845090822 8.057539790554989 chrX 155270560 48490574 0.3122972828847915 1.198655671211419 chrY 59373566 2017668 0.03398259757549344 0.5525109121787062